WO2020112601A1 - Small-scale robots for biofilm eradication - Google Patents

Small-scale robots for biofilm eradication Download PDF

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Publication number
WO2020112601A1
WO2020112601A1 PCT/US2019/062941 US2019062941W WO2020112601A1 WO 2020112601 A1 WO2020112601 A1 WO 2020112601A1 US 2019062941 W US2019062941 W US 2019062941W WO 2020112601 A1 WO2020112601 A1 WO 2020112601A1
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WO
WIPO (PCT)
Prior art keywords
biofilm
iron oxide
oxide nanoparticles
matrix
biohybrid
Prior art date
Application number
PCT/US2019/062941
Other languages
French (fr)
Inventor
Hyun Koo
Kathleen STEBE
Vijay Kumar
Elizabeth Hunter
Edward Steager
Evan BRINK
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The Trustees Of The University Of Pennsylvania
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority to BR112021010037-7A priority Critical patent/BR112021010037A2/en
Priority to US17/291,326 priority patent/US20220000119A1/en
Priority to CN201980078197.1A priority patent/CN113194727A/en
Priority to CA3119489A priority patent/CA3119489A1/en
Priority to EP19890194.4A priority patent/EP3886589A4/en
Priority to JP2021530103A priority patent/JP2022510910A/en
Application filed by The Trustees Of The University Of Pennsylvania filed Critical The Trustees Of The University Of Pennsylvania
Priority to KR1020217019435A priority patent/KR20210098480A/en
Priority to MX2021006072A priority patent/MX2021006072A/en
Priority to IL283393A priority patent/IL283393B1/en
Priority to AU2019388848A priority patent/AU2019388848A1/en
Publication of WO2020112601A1 publication Critical patent/WO2020112601A1/en
Priority to ZA2021/04331A priority patent/ZA202104331B/en

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    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01N—PRESERVATION OF BODIES OF HUMANS OR ANIMALS OR PLANTS OR PARTS THEREOF; BIOCIDES, e.g. AS DISINFECTANTS, AS PESTICIDES OR AS HERBICIDES; PEST REPELLANTS OR ATTRACTANTS; PLANT GROWTH REGULATORS
    • A01N59/00—Biocides, pest repellants or attractants, or plant growth regulators containing elements or inorganic compounds
    • A01N59/16—Heavy metals; Compounds thereof
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01N—PRESERVATION OF BODIES OF HUMANS OR ANIMALS OR PLANTS OR PARTS THEREOF; BIOCIDES, e.g. AS DISINFECTANTS, AS PESTICIDES OR AS HERBICIDES; PEST REPELLANTS OR ATTRACTANTS; PLANT GROWTH REGULATORS
    • A01N59/00—Biocides, pest repellants or attractants, or plant growth regulators containing elements or inorganic compounds
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01N—PRESERVATION OF BODIES OF HUMANS OR ANIMALS OR PLANTS OR PARTS THEREOF; BIOCIDES, e.g. AS DISINFECTANTS, AS PESTICIDES OR AS HERBICIDES; PEST REPELLANTS OR ATTRACTANTS; PLANT GROWTH REGULATORS
    • A01N25/00—Biocides, pest repellants or attractants, or plant growth regulators, characterised by their forms, or by their non-active ingredients or by their methods of application, e.g. seed treatment or sequential application; Substances for reducing the noxious effect of the active ingredients to organisms other than pests
    • A01N25/02—Biocides, pest repellants or attractants, or plant growth regulators, characterised by their forms, or by their non-active ingredients or by their methods of application, e.g. seed treatment or sequential application; Substances for reducing the noxious effect of the active ingredients to organisms other than pests containing liquids as carriers, diluents or solvents
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
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    • A01N25/00—Biocides, pest repellants or attractants, or plant growth regulators, characterised by their forms, or by their non-active ingredients or by their methods of application, e.g. seed treatment or sequential application; Substances for reducing the noxious effect of the active ingredients to organisms other than pests
    • A01N25/02—Biocides, pest repellants or attractants, or plant growth regulators, characterised by their forms, or by their non-active ingredients or by their methods of application, e.g. seed treatment or sequential application; Substances for reducing the noxious effect of the active ingredients to organisms other than pests containing liquids as carriers, diluents or solvents
    • A01N25/04—Dispersions, emulsions, suspoemulsions, suspension concentrates or gels
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01N—PRESERVATION OF BODIES OF HUMANS OR ANIMALS OR PLANTS OR PARTS THEREOF; BIOCIDES, e.g. AS DISINFECTANTS, AS PESTICIDES OR AS HERBICIDES; PEST REPELLANTS OR ATTRACTANTS; PLANT GROWTH REGULATORS
    • A01N25/00—Biocides, pest repellants or attractants, or plant growth regulators, characterised by their forms, or by their non-active ingredients or by their methods of application, e.g. seed treatment or sequential application; Substances for reducing the noxious effect of the active ingredients to organisms other than pests
    • A01N25/34—Shaped forms, e.g. sheets, not provided for in any other sub-group of this main group
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01N—PRESERVATION OF BODIES OF HUMANS OR ANIMALS OR PLANTS OR PARTS THEREOF; BIOCIDES, e.g. AS DISINFECTANTS, AS PESTICIDES OR AS HERBICIDES; PEST REPELLANTS OR ATTRACTANTS; PLANT GROWTH REGULATORS
    • A01N63/00—Biocides, pest repellants or attractants, or plant growth regulators containing microorganisms, viruses, microbial fungi, animals or substances produced by, or obtained from, microorganisms, viruses, microbial fungi or animals, e.g. enzymes or fermentates
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    • A61K9/51—Nanocapsules; Nanoparticles
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    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/24—Hydrolases (3) acting on glycosyl compounds (3.2)
    • C12N9/2402—Hydrolases (3) acting on glycosyl compounds (3.2) hydrolysing O- and S- glycosyl compounds (3.2.1)
    • C12N9/2405—Glucanases
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N9/14—Hydrolases (3)
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    • C12N9/2405—Glucanases
    • C12N9/2451—Glucanases acting on alpha-1,6-glucosidic bonds
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    • F—MECHANICAL ENGINEERING; LIGHTING; HEATING; WEAPONS; BLASTING
    • F03—MACHINES OR ENGINES FOR LIQUIDS; WIND, SPRING, OR WEIGHT MOTORS; PRODUCING MECHANICAL POWER OR A REACTIVE PROPULSIVE THRUST, NOT OTHERWISE PROVIDED FOR
    • F03G—SPRING, WEIGHT, INERTIA OR LIKE MOTORS; MECHANICAL-POWER PRODUCING DEVICES OR MECHANISMS, NOT OTHERWISE PROVIDED FOR OR USING ENERGY SOURCES NOT OTHERWISE PROVIDED FOR
    • F03G7/00—Mechanical-power-producing mechanisms, not otherwise provided for or using energy sources not otherwise provided for
    • F03G7/008—Mechanical-power-producing mechanisms, not otherwise provided for or using energy sources not otherwise provided for characterised by the actuating element
    • F03G7/017—Actuators comprising biological materials
    • H—ELECTRICITY
    • H01—ELECTRIC ELEMENTS
    • H01F—MAGNETS; INDUCTANCES; TRANSFORMERS; SELECTION OF MATERIALS FOR THEIR MAGNETIC PROPERTIES
    • H01F1/00—Magnets or magnetic bodies characterised by the magnetic materials therefor; Selection of materials for their magnetic properties
    • H01F1/01—Magnets or magnetic bodies characterised by the magnetic materials therefor; Selection of materials for their magnetic properties of inorganic materials
    • H01F1/03—Magnets or magnetic bodies characterised by the magnetic materials therefor; Selection of materials for their magnetic properties of inorganic materials characterised by their coercivity
    • H01F1/12—Magnets or magnetic bodies characterised by the magnetic materials therefor; Selection of materials for their magnetic properties of inorganic materials characterised by their coercivity of soft-magnetic materials
    • H01F1/34—Magnets or magnetic bodies characterised by the magnetic materials therefor; Selection of materials for their magnetic properties of inorganic materials characterised by their coercivity of soft-magnetic materials non-metallic substances, e.g. ferrites
    • H01F1/36—Magnets or magnetic bodies characterised by the magnetic materials therefor; Selection of materials for their magnetic properties of inorganic materials characterised by their coercivity of soft-magnetic materials non-metallic substances, e.g. ferrites in the form of particles
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Definitions

  • Bio films are structured communities of bacterial cells surrounded by a matrix of extracellular polymeric substances attached to a surface.
  • Biofilms can be formed on biotic surfaces such as teeth and mucosal surfaces, as well as abiotic surfaces such as implanted medical devices and catheters, thereby leading to infections and medical complications in patients.
  • Biofilms can also exist in natural and industrial settings. For example, biofilms can contaminate man-made aquatic systems such as cooling towers, pools and spas. In the industrial setting, biofilms can develop on the interiors of pipes that can lead to clogs and corrosion.
  • the extracellular matrix of such biofilms can contain polymeric substances, such as exopolysaccharides (EPS), which is a complex and mechanically stable scaffold that provides cohesion/adhesion and acts as a barrier to antibacterial drugs, protecting bacteria within them.
  • EPS exopolysaccharides
  • Certain techniques for combating biofilms are largely ineffective because they fail to both eradicate and remove biofilms, which leads to reinfection.
  • Antimicrobial approaches such as antibiotics and immune responses, can fail to address the complex structural and biological properties of bio film, and the biofilm retains the ability to rapidly reestablish itself if biofilm debris and bacteria are not removed.
  • the disclosed subject matter provides techniques for administering a suspension of H2O2 and iron oxide nanoparticles to substantially eradicate bacteria within a biofilm matrix and degrade the biofilm matrix, actuating the iron oxide nanoparticles for assembly into biohybrid robots suitable for removal of biofilm debris caused by biofilm degradation, and moving the biohybrid robots to remove the biofilm debris from a surface.
  • the suspension can be formulated with between 500 micrograms and 5000 micrograms of iron oxide nanoparticles per milliliter of 50% glycerol.
  • the suspension can be formulated with enzymes, including mutanase, dextranase, DNase, protease, lipase, amyloglucosidade, glucose oxidase, or combinations thereof, to degrade the biofilm matrix.
  • enzymes including mutanase, dextranase, DNase, protease, lipase, amyloglucosidade, glucose oxidase, or combinations thereof, to degrade the biofilm matrix.
  • the suspension can be formulated with 1% H2O2 and 1.75U/8.75U mutanase/ dextranase to substantially eradicate the bacteria and degrade the biofilm matrix.
  • a permanent magnet or an array of electromagnets can apply a magnetic field from the permanent magnet to the biofilm to actuate the iron oxide nanoparticles to assemble into biohybrid robots.
  • the magnetic field can move the biohybrid robots to remove the biofilm debris from a surface (e.g . , biofilm removal from biotic and abiotic surfaces, including dental, dentures, implants, windows or other glass, plastic surfaces where biofilms can form).
  • the disclosed subject matter can include embedding iron oxide nanoparticles in a hydrogel to form a soft robotic structure to performed specific tasks to remove biofilms from enclosed surfaces.
  • the hydrogel can be a stimuli-responsive polymer.
  • the soft robotic structure can be 3% weight by volume agar and 10% weight by volume iron oxide nanoparticles.
  • the soft robotic structure which can realign with a magnetic field direction, can be magnetized along its short axis.
  • the soft robotic structure can be vane-shaped to scrape biofilms from a wall of an enclosed surface and displace the biofilm debris.
  • the soft robotic structure can be double helicoid shaped to drill through biofilm occlusions and clear biofilm from walls.
  • the disclosed techniques can be applied to eradicate bacteria within a biofilm matrix, degrade the matrix and remove biofilm debris on biotic surfaces such as teeth and mucosal surfaces, as well as abiotic surfaces such as implanted medical devices and catheters, or surgical instruments including endoscopes, cannul as/cannul ae thereby preventing infections and medical complications in patients.
  • the disclosed techniques can be applied to eradicate bacteria within a biofilm matrix, degrade the matrix and remove biofilm debris in natural and industrial settings such as man-made aquatic systems (e.g ., cooling towers, pools, aquariums and spas), glass/plastic surfaces including windows and food packaging and the interiors of pipes, water lines and other enclosed surfaces.
  • man-made aquatic systems e.g ., cooling towers, pools, aquariums and spas
  • glass/plastic surfaces including windows and food packaging and the interiors of pipes, water lines and other enclosed surfaces.
  • FIG. 1 is a diagram illustrating the dual catalytic-magnetic functionality of the iron oxide nanoparticles.
  • FIG. 2 is a diagram illustrating the application of a suspension of the iron oxide nanoparticles on biofilm.
  • FIG. 3 depicts the dose dependent eradication activity of the iron oxide nanoparticles.
  • FIG. 4 depicts the dose dependent extracellular matrix degradation of the enzymes mutanase and dextranase.
  • FIG. 5 is a diagram illustrating two platforms for the iron oxide nanoparticles.
  • FIGS. 6A-6E depicts bacterial regrowth with and without the removal of the bio film debris.
  • FIG. 7 illustrates iron oxide nanoparticles being manipulated by a magnetic element.
  • FIG. 8 is a diagram illustrating the removal of large areas of biofilm debris by magnetically-controlled movement of the iron oxide nanoparticles.
  • FIG. 9 illustrates the controlled movements of the iron oxide nanoparticles over well-defined paths with micrometer scale geometric precision.
  • FIG. 10 illustrates model representations of a vane-shaped soft robotic structure and a double helicoid-shaped soft robotic structure.
  • FIG. 11 is a diagram illustrating the vane-shaped soft robotic structure cleaning bio film on the wall of a cylindrical tube.
  • FIG. 12 is a diagram illustrating the double helicoid-shaped soft robotic structure drilling through a biofilm clog in a cylindrical tube.
  • FIGS. 13A-C depict an example of the use of iron oxide nanoparticles for endodontic disinfection and to treat biofilm in the tooth canal.
  • the iron oxide nanoparticles are administered to a biofilm-covered surface in a suspension or as a soft robotic structure. Once the iron oxide nanoparticles are administered, the catalytic function of the iron oxide nanoparticles substantially eradicates the bacteria and degrades the biofilm matrix. The magnetic function of the iron oxide nanoparticles is activated to actuate the iron oxide nanoparticles for assembly suitable for removal of the biofilm debris.
  • FIG. 1 is a diagram illustrating the dual catalytic-magnetic functionality of the iron oxide nanoparticles in accordance with an embodiment of disclosed subject matter.
  • the iron oxide nanoparticles 101 can catalyze hydrogen peroxide (H2O2) to substantially eradicate the bacteria 102 and degrade the biofilm matrix 103.
  • H2O2 hydrogen peroxide
  • the biofilm matrix degradation is key for disrupting the structural scaffold while also facilitating penetration and bacterial eradication.
  • the bacterial eradication effect is substantially enhanced when the biofilm matrix is degraded.
  • the biofilm matrix is degraded when it is sufficiently broken down to allow for bacterial eradication.
  • the bacteria is substantially eradicated when the bacteria within the biofilm matrix is killed.
  • the iron oxide nanoparticles can be magnetically activated 104 to actuate the iron oxide nanoparticles for assembly into biohybrid robots and to move the biohybrid robots to remove the biofilm debris from a surface.
  • FIG. 2 is a diagram illustrating the application of a suspension of the iron oxide nanoparticles on biofilm in accordance with an embodiment of disclosed subject matter.
  • the iron oxide nanoparticles catalyze hydrogen peroxide (H2O2) to generate free radicals. These free radicals can substantially eradicate the bacteria embedded within a biofilm extracellular matrix.
  • the free radicals can also degrade the biofilm extracellular matrix. This degradation occurs more slowly than the free radicals substantially eradicate the bacteria.
  • FIG. 3 depicts the dose dependent eradication activity of the iron oxide nanoparticles in accordance with an embodiment of disclosed subject matter.
  • a concentration of between 500 micrograms and 5000 of iron oxide nanoparticles per milliliter of 50% glycerol achieves maximal efficacy for eradicating the bacteria.
  • FIG. 4 depicts the dose dependent extracellular matrix degradation of the enzymes mutanase and dextranase in accordance with an embodiment of disclosed subject matter. While the catalytic function of iron oxide nanoparticles degrades the biofilm matrix more slowly than it substantially eradicates the bacteria, the rate of degradation can be enhanced with enzymes including mutanase and dextranase. A combination of 1.75U mutanase and 8.75U dextranase achieves maximal efficacy for extracellular matrix degradation.
  • FIG. 5 is a diagram illustrating two example platforms for the iron oxide nanoparticles in accordance with an embodiment of disclosed subject matter. These platforms enable the iron oxide nanoparticles to remove the biofilm debris.
  • the iron oxide nanoparticles 501 are suspended and administered to a biofilm- covered surface. Once the iron oxide nanoparticles perform their catalytic function, they are actuated for assembly into biohybrid robots 502 using a magnetic element.
  • the magnetic element can be a permanent magnet or an an array of electromagnets that applies a magnetic field.
  • the iron oxide nanoparticles are embedded in a hydrogel to form a soft robotic structure 503. In some embodiments, these structures can be vane-shaped 504 or double-helicoid-shaped 505.
  • the shape of the structures can enable eradication of bio film from confined and inaccessible locations.
  • FIGS. 6A-6E depicts bacterial regrowth with and without the removal of the biofilm debris in accordance with an embodiment of disclosed subject matter.
  • a biofilm-covered surface was not treated with iron oxide nanoparticles.
  • FIG. 6B a biofilm-covered surface was treated with iron oxide nanoparticles, but the biofilm debris was not removed from the surface.
  • FIGS. 6A and 6B both show biofilm regrowth, demonstrating that biofilm retains the ability to rapidly reestablish itself if the biofilm debris is not removed.
  • FIG. 6C a biofilm-covered surface was treated with iron oxide nanoparticles and the biofilm debris was removed from the surface via magnetic actuation. No biofilm regrowth was observed in FIG 6C.
  • FIGS. 6A-6C show the amount of biomass and viable cells, respectively, on the surfaces in FIGS. 6A-6C.
  • the surfaces in both FIG. 6A and 6B show a high level of biomass and viable cells, whereas the surface in FIG. 6C shows no detected biomass or viable cells.
  • FIG. 7 illustrates iron oxide nanoparticles being manipulated by a magnetic element in accordance with an embodiment of disclosed subject matter.
  • the magnetic element is activated 702.
  • the magnetic element actuates the iron oxide nanoparticles for assembly into biohybrid robots 703 and controls the movement of the biohybrid robots 703.
  • the biohybrid robots can form rod-like structures 704 that can remove the biofilm debris by penetrating the biofilm debris and incorporating the biofilm debris into the biohybrid robots.
  • FIG. 8 is a diagram illustrating the removal of large areas of biofilm debris by magnetically-controlled movement of the biohybrid robots in accordance with an embodiment of disclosed subject matter.
  • the biohybrid robots can move over broad swathes of the biofilm-covered surface.
  • the biohybrid robots can follow a defined trajectory that starts at the center of the biofilm-covered surface and progressively moves outward in a concentric manner. Following this trajectory, the biohybrid robots can clear the biofilm debris away from the contaminated surface. This trajectory can also continually pull individual iron oxide nanoparticles into the superstructure, thereby increasing its size and density.
  • FIG. 9 illustrates the controlled movements of the biohybrid robots over well- defined paths with micrometer scale geometric precision in accordance with an embodiment of disclosed subject matter.
  • the biohybrid robots 901 can move over well- defined paths 902 with micrometer scale geometric precision 903.
  • biofilms can be removed without damaging nearby host-tissues or biofilms can be sampled at specific pathological sites.
  • the suspension of iron oxide nanoparticles can be concentrated near a biofilm-covered surface to enable localized bio film eradication.
  • FIG. 10 illustrates model representations of a vane-shaped soft robotic structure and a double helicoid-shaped soft robotic structure in accordance with an embodiment of disclosed subject matter.
  • the iron oxide nanoparticles are embedded in a hydrogel to form a soft robotic structure. These structures can be shaped to perform specific tasks such as the eradication of biofilm from confined and inaccessible locations.
  • the hydrogel can be permeable to H2O2, so the iron oxide nanoparticles can perform their catalytic function as described above.
  • the hydrogel can be a stimuli-responsive polymer.
  • the hydrogel can be a thermos-reversible gelifying agar polymer, or another stimuli-responsive polymer, including pH and temperature -responsive polymers.
  • the soft robotic structure can be 3% weight per volume agar and 10% weight per volume iron oxide nanoparticles.
  • both structures can be magnetized along their short axis to realign with a magnetic field direction.
  • FIG. 11 is a diagram illustrating the vane-shaped soft robotic structure cleaning biofilm on the wall of a cylindrical tube in accordance with an embodiment of disclosed subject matter.
  • the vane shape can have a central core with fin-like structures.
  • the vane shaped structure 1101 can rotate with an applied magnetic torque from a magnetic element can move forward at a velocity by applying a force using the magnetic element. This rotation can generate localized fluid shear stress and scrub the curved surface of a tube 1102. As the vane-shaped structure moves forward, it sweeps over the curved surface, thereby scraping and displacing biofilm debris.
  • the displaced biofilm debris forms a pile 1103 that can be removed from the tube by flushing it with water.
  • FIG. 12 is a diagram illustrating the double helicoid-shaped soft robotic structure drilling through a biofilm clog in a cylindrical tube in accordance with an embodiment of disclosed subject matter.
  • the double helicoid shape can have two helices wrapped around a central axis.
  • the chiral geometry of the double helicoid-shaped structure 1201 enables it to move forward with an applied magnetic torque from a magnetic element, thereby propelling the structure in a corkscrew-like fashion 1202. Due to this motion, the double helicoid-shaped structure can drill through biofilm occlusions 1203 and clear biofilms from walls. As the structure moves forward, it forms a pile that can be removed from the tube by flushing it with water.
  • FIGS. 13A-C depict an example of the use of biohybrid robots to treat biofilm in the tooth canal in accordance with an embodiment of disclosed subject matter.
  • FIGS. 13A and 13B depict cross-sectional views of the tooth canal.
  • FIG. 13A depicts an example of the use of biohybrid robots to treat biofilm in the tooth canal in accordance with an embodiment of disclosed subject matter.
  • FIGS. 13A and 13B depict cross-sectional views of the tooth canal.
  • iron oxide nanoparticles can be administered to an isthmus, a narrow corridor of approximately 200 to 600 micrometers in width between two root canals, and actuated for assembly into biohybrid robots that can then be moved from one end to another, transversing the entire extent of the isthmus.
  • double helicoid shaped soft robotic structure made of iron oxide nanoparticles can also be magnetically controlled across the extent of the tooth canal (Fig 13B).
  • FIG. 13B shows a latitudinal section of the tooth canal.
  • the double helicoid-shaped soft robot is at a top of the tooth canal.
  • FIG. 13C depicts the eradication of biofilm in the isthmus by biohybrid robots as shown before and after treatment; the biofilms were fluorescently labelled for
  • the disclosed techniques can be applied to eradicate bacteria within a biofilm matrix, degrade the matrix and remove biofilm debris on biotic surfaces such as teeth and mucosal surfaces, as well as abiotic surfaces such as implanted medical devices and catheters, or surgical instruments including endoscopes, cannulas/cannulae thereby preventing infections and medical complications in patients.
  • the disclosed techniques can be applied to eradicate bacteria within a biofilm matrix, degrade the matrix and remove biofilm debris in natural and industrial settings such as man-made aquatic systems (e.g ., cooling towers, pools, aquariums and spas), glass/plastic surfaces including windows and food packaging and the interiors of pipes, water lines and other enclosed surfaces.

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Abstract

Systems and methods for eradicating biofilms by killing bacteria within a biofilm, degrading the matrix and removing biofilm debris are disclosed herein. The disclosed subject matter provides techniques for administering a suspension of H2O2 and iron oxide nanoparticles to substantially eradicate bacteria within a biofilm matrix and degrade the bio film matrix, actuating the iron oxide nanoparticles for assembly into biohybrid robots suitable for removal of biofilm debris, and moving the biohybrid robots to remove the bio film debris from accessible or enclosed surfaces. In some embodiments, the disclosed subject matter can include embedding iron oxide nanoparticles in a hydrogel to form a soft robotic structure, administering the soft robotic structure to a biofilm-covered location, and magnetizing the soft robot structure to substantially eradicate bacteria within a biofilm matrix, degrade the biofilm matrix, and remove biofilm debris from enclosed surfaces.

Description

SMALL-SCALE ROBOTS FOR BIOFILM ERADICATION
STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH
This invention was made with government support under grant number R01 DE025848 awarded by the National Institutes of Health (NIH). The government has certain rights in the invention.
CROSS-REFERENCE TO RELATED APPLICATIONS
This application claims priority from U.S. Provisional Patent No. 62/772,306, filed November 28, 2018, which is incorporated by reference herein.
BACKGROUND
Bio films are structured communities of bacterial cells surrounded by a matrix of extracellular polymeric substances attached to a surface. Biofilms can be formed on biotic surfaces such as teeth and mucosal surfaces, as well as abiotic surfaces such as implanted medical devices and catheters, thereby leading to infections and medical complications in patients. Biofilms can also exist in natural and industrial settings. For example, biofilms can contaminate man-made aquatic systems such as cooling towers, pools and spas. In the industrial setting, biofilms can develop on the interiors of pipes that can lead to clogs and corrosion. The extracellular matrix of such biofilms can contain polymeric substances, such as exopolysaccharides (EPS), which is a complex and mechanically stable scaffold that provides cohesion/adhesion and acts as a barrier to antibacterial drugs, protecting bacteria within them.
Certain techniques for combating biofilms are largely ineffective because they fail to both eradicate and remove biofilms, which leads to reinfection. Antimicrobial approaches, such as antibiotics and immune responses, can fail to address the complex structural and biological properties of bio film, and the biofilm retains the ability to rapidly reestablish itself if biofilm debris and bacteria are not removed.
Accordingly, there exists a need for a technique to effectively substantially eradicate bacteria within a biofilm matrix, degrade the biofilm matrix, and remove any resulting biofilm debris. SUMMARY
Systems and methods using small-scale robotics to eradicate bacteria within a biofilm matrix are disclosed herein.
The disclosed subject matter provides techniques for administering a suspension of H2O2 and iron oxide nanoparticles to substantially eradicate bacteria within a biofilm matrix and degrade the biofilm matrix, actuating the iron oxide nanoparticles for assembly into biohybrid robots suitable for removal of biofilm debris caused by biofilm degradation, and moving the biohybrid robots to remove the biofilm debris from a surface. In some embodiments, the suspension can be formulated with between 500 micrograms and 5000 micrograms of iron oxide nanoparticles per milliliter of 50% glycerol. In some embodiments, the suspension can be formulated with enzymes, including mutanase, dextranase, DNase, protease, lipase, amyloglucosidade, glucose oxidase, or combinations thereof, to degrade the biofilm matrix. For example, the suspension can be formulated with 1% H2O2 and 1.75U/8.75U mutanase/ dextranase to substantially eradicate the bacteria and degrade the biofilm matrix.
In some embodiments, a permanent magnet or an array of electromagnets can apply a magnetic field from the permanent magnet to the biofilm to actuate the iron oxide nanoparticles to assemble into biohybrid robots. In some embodiments, the magnetic field can move the biohybrid robots to remove the biofilm debris from a surface ( e.g . , biofilm removal from biotic and abiotic surfaces, including dental, dentures, implants, windows or other glass, plastic surfaces where biofilms can form).
In some embodiments, the disclosed subject matter can include embedding iron oxide nanoparticles in a hydrogel to form a soft robotic structure to performed specific tasks to remove biofilms from enclosed surfaces. In some embodiments, the hydrogel can be a stimuli-responsive polymer. The soft robotic structure can be 3% weight by volume agar and 10% weight by volume iron oxide nanoparticles. For example, the soft robotic structure, which can realign with a magnetic field direction, can be magnetized along its short axis.
In some embodiments of the disclosed subject matter, the soft robotic structure can be vane-shaped to scrape biofilms from a wall of an enclosed surface and displace the biofilm debris. In some embodiments, the soft robotic structure can be double helicoid shaped to drill through biofilm occlusions and clear biofilm from walls. The disclosed techniques can be applied to eradicate bacteria within a biofilm matrix, degrade the matrix and remove biofilm debris on biotic surfaces such as teeth and mucosal surfaces, as well as abiotic surfaces such as implanted medical devices and catheters, or surgical instruments including endoscopes, cannul as/cannul ae thereby preventing infections and medical complications in patients. Furthermore, the disclosed techniques can be applied to eradicate bacteria within a biofilm matrix, degrade the matrix and remove biofilm debris in natural and industrial settings such as man-made aquatic systems ( e.g ., cooling towers, pools, aquariums and spas), glass/plastic surfaces including windows and food packaging and the interiors of pipes, water lines and other enclosed surfaces.
The accompanying drawings, which are incorporated and constitute part of this disclosure, illustrate preferred embodiments of the invention and serve to explain the principles of the invention.
BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 is a diagram illustrating the dual catalytic-magnetic functionality of the iron oxide nanoparticles.
FIG. 2 is a diagram illustrating the application of a suspension of the iron oxide nanoparticles on biofilm.
FIG. 3 depicts the dose dependent eradication activity of the iron oxide nanoparticles.
FIG. 4 depicts the dose dependent extracellular matrix degradation of the enzymes mutanase and dextranase.
FIG. 5 is a diagram illustrating two platforms for the iron oxide nanoparticles.
FIGS. 6A-6E depicts bacterial regrowth with and without the removal of the bio film debris.
FIG. 7 illustrates iron oxide nanoparticles being manipulated by a magnetic element.
FIG. 8 is a diagram illustrating the removal of large areas of biofilm debris by magnetically-controlled movement of the iron oxide nanoparticles.
FIG. 9 illustrates the controlled movements of the iron oxide nanoparticles over well-defined paths with micrometer scale geometric precision.
FIG. 10 illustrates model representations of a vane-shaped soft robotic structure and a double helicoid-shaped soft robotic structure. FIG. 11 is a diagram illustrating the vane-shaped soft robotic structure cleaning bio film on the wall of a cylindrical tube.
FIG. 12 is a diagram illustrating the double helicoid-shaped soft robotic structure drilling through a biofilm clog in a cylindrical tube.
FIGS. 13A-C depict an example of the use of iron oxide nanoparticles for endodontic disinfection and to treat biofilm in the tooth canal.
Throughout the drawings, the same reference numerals and characters, unless otherwise stated, are used to denote like features, elements, components or portions of the illustrated embodiments. Moreover, while the present invention will now be described in detail with reference to the Figs., it is done so in connection with the illustrative embodiments.
DETAILED DESCRIPTION
Techniques for eradicating biofilms using iron oxide nanoparticles to substantially eradicate bacteria within a biofilm matrix, degrade the biofilm matrix, and remove biofilm debris caused by biofilm eradication are presented. The iron oxide nanoparticles are administered to a biofilm-covered surface in a suspension or as a soft robotic structure. Once the iron oxide nanoparticles are administered, the catalytic function of the iron oxide nanoparticles substantially eradicates the bacteria and degrades the biofilm matrix. The magnetic function of the iron oxide nanoparticles is activated to actuate the iron oxide nanoparticles for assembly suitable for removal of the biofilm debris.
FIG. 1 is a diagram illustrating the dual catalytic-magnetic functionality of the iron oxide nanoparticles in accordance with an embodiment of disclosed subject matter. The iron oxide nanoparticles 101 can catalyze hydrogen peroxide (H2O2) to substantially eradicate the bacteria 102 and degrade the biofilm matrix 103. The biofilm matrix degradation is key for disrupting the structural scaffold while also facilitating penetration and bacterial eradication. The bacterial eradication effect is substantially enhanced when the biofilm matrix is degraded. The biofilm matrix is degraded when it is sufficiently broken down to allow for bacterial eradication. The bacteria is substantially eradicated when the bacteria within the biofilm matrix is killed. The iron oxide nanoparticles can be magnetically activated 104 to actuate the iron oxide nanoparticles for assembly into biohybrid robots and to move the biohybrid robots to remove the biofilm debris from a surface. FIG. 2 is a diagram illustrating the application of a suspension of the iron oxide nanoparticles on biofilm in accordance with an embodiment of disclosed subject matter. The iron oxide nanoparticles catalyze hydrogen peroxide (H2O2) to generate free radicals. These free radicals can substantially eradicate the bacteria embedded within a biofilm extracellular matrix. The free radicals can also degrade the biofilm extracellular matrix. This degradation occurs more slowly than the free radicals substantially eradicate the bacteria.
FIG. 3 depicts the dose dependent eradication activity of the iron oxide nanoparticles in accordance with an embodiment of disclosed subject matter. A concentration of between 500 micrograms and 5000 of iron oxide nanoparticles per milliliter of 50% glycerol achieves maximal efficacy for eradicating the bacteria.
FIG. 4 depicts the dose dependent extracellular matrix degradation of the enzymes mutanase and dextranase in accordance with an embodiment of disclosed subject matter. While the catalytic function of iron oxide nanoparticles degrades the biofilm matrix more slowly than it substantially eradicates the bacteria, the rate of degradation can be enhanced with enzymes including mutanase and dextranase. A combination of 1.75U mutanase and 8.75U dextranase achieves maximal efficacy for extracellular matrix degradation.
FIG. 5 is a diagram illustrating two example platforms for the iron oxide nanoparticles in accordance with an embodiment of disclosed subject matter. These platforms enable the iron oxide nanoparticles to remove the biofilm debris. In the first platform, the iron oxide nanoparticles 501 are suspended and administered to a biofilm- covered surface. Once the iron oxide nanoparticles perform their catalytic function, they are actuated for assembly into biohybrid robots 502 using a magnetic element. In some embodiments, the magnetic element can be a permanent magnet or an an array of electromagnets that applies a magnetic field. In the second platform, the iron oxide nanoparticles are embedded in a hydrogel to form a soft robotic structure 503. In some embodiments, these structures can be vane-shaped 504 or double-helicoid-shaped 505.
The shape of the structures can enable eradication of bio film from confined and inaccessible locations.
FIGS. 6A-6E depicts bacterial regrowth with and without the removal of the biofilm debris in accordance with an embodiment of disclosed subject matter. In FIG. 6A, a biofilm-covered surface was not treated with iron oxide nanoparticles. In FIG. 6B, a biofilm-covered surface was treated with iron oxide nanoparticles, but the biofilm debris was not removed from the surface. FIGS. 6A and 6B both show biofilm regrowth, demonstrating that biofilm retains the ability to rapidly reestablish itself if the biofilm debris is not removed. In FIG. 6C, a biofilm-covered surface was treated with iron oxide nanoparticles and the biofilm debris was removed from the surface via magnetic actuation. No biofilm regrowth was observed in FIG 6C. FIGS. 6D and 6E show the amount of biomass and viable cells, respectively, on the surfaces in FIGS. 6A-6C. The surfaces in both FIG. 6A and 6B show a high level of biomass and viable cells, whereas the surface in FIG. 6C shows no detected biomass or viable cells.
FIG. 7 illustrates iron oxide nanoparticles being manipulated by a magnetic element in accordance with an embodiment of disclosed subject matter. Once the iron oxide nanoparticles 701 substantially eradicate the bacteria and degrade the biofilm matrix, the magnetic element is activated 702. The magnetic element actuates the iron oxide nanoparticles for assembly into biohybrid robots 703 and controls the movement of the biohybrid robots 703. In some embodiment, the biohybrid robots can form rod-like structures 704 that can remove the biofilm debris by penetrating the biofilm debris and incorporating the biofilm debris into the biohybrid robots.
FIG. 8 is a diagram illustrating the removal of large areas of biofilm debris by magnetically-controlled movement of the biohybrid robots in accordance with an embodiment of disclosed subject matter. The biohybrid robots can move over broad swathes of the biofilm-covered surface. In some embodiments, the biohybrid robots can follow a defined trajectory that starts at the center of the biofilm-covered surface and progressively moves outward in a concentric manner. Following this trajectory, the biohybrid robots can clear the biofilm debris away from the contaminated surface. This trajectory can also continually pull individual iron oxide nanoparticles into the superstructure, thereby increasing its size and density.
FIG. 9 illustrates the controlled movements of the biohybrid robots over well- defined paths with micrometer scale geometric precision in accordance with an embodiment of disclosed subject matter. The biohybrid robots 901 can move over well- defined paths 902 with micrometer scale geometric precision 903. For example, biofilms can be removed without damaging nearby host-tissues or biofilms can be sampled at specific pathological sites. In some embodiments, the suspension of iron oxide nanoparticles can be concentrated near a biofilm-covered surface to enable localized bio film eradication. FIG. 10 illustrates model representations of a vane-shaped soft robotic structure and a double helicoid-shaped soft robotic structure in accordance with an embodiment of disclosed subject matter. The iron oxide nanoparticles are embedded in a hydrogel to form a soft robotic structure. These structures can be shaped to perform specific tasks such as the eradication of biofilm from confined and inaccessible locations. The hydrogel can be permeable to H2O2, so the iron oxide nanoparticles can perform their catalytic function as described above. In some embodiments, the hydrogel can be a stimuli-responsive polymer. For example, the hydrogel can be a thermos-reversible gelifying agar polymer, or another stimuli-responsive polymer, including pH and temperature -responsive polymers. In some embodiments, the soft robotic structure can be 3% weight per volume agar and 10% weight per volume iron oxide nanoparticles. In some embodiments, both structures can be magnetized along their short axis to realign with a magnetic field direction.
FIG. 11 is a diagram illustrating the vane-shaped soft robotic structure cleaning biofilm on the wall of a cylindrical tube in accordance with an embodiment of disclosed subject matter. The vane shape can have a central core with fin-like structures. The vane shaped structure 1101 can rotate with an applied magnetic torque from a magnetic element can move forward at a velocity by applying a force using the magnetic element. This rotation can generate localized fluid shear stress and scrub the curved surface of a tube 1102. As the vane-shaped structure moves forward, it sweeps over the curved surface, thereby scraping and displacing biofilm debris. The displaced biofilm debris forms a pile 1103 that can be removed from the tube by flushing it with water.
FIG. 12 is a diagram illustrating the double helicoid-shaped soft robotic structure drilling through a biofilm clog in a cylindrical tube in accordance with an embodiment of disclosed subject matter. The double helicoid shape can have two helices wrapped around a central axis. The chiral geometry of the double helicoid-shaped structure 1201 enables it to move forward with an applied magnetic torque from a magnetic element, thereby propelling the structure in a corkscrew-like fashion 1202. Due to this motion, the double helicoid-shaped structure can drill through biofilm occlusions 1203 and clear biofilms from walls. As the structure moves forward, it forms a pile that can be removed from the tube by flushing it with water.
FIGS. 13A-C depict an example of the use of biohybrid robots to treat biofilm in the tooth canal in accordance with an embodiment of disclosed subject matter. In particular, FIGS. 13A and 13B depict cross-sectional views of the tooth canal. In FIG.
13 A, iron oxide nanoparticles can be administered to an isthmus, a narrow corridor of approximately 200 to 600 micrometers in width between two root canals, and actuated for assembly into biohybrid robots that can then be moved from one end to another, transversing the entire extent of the isthmus. As shown in FIG. 13B, double helicoid shaped soft robotic structure made of iron oxide nanoparticles can also be magnetically controlled across the extent of the tooth canal (Fig 13B). FIG. 13A shows a longitudinal cross-section of the tooth canal. At t=0s, the biohybrid robot is in one of the root canals. At t=l 1.5s, the biohybrid robot passes through the isthmus. At t— 14.5s, the biohybrid robot reaches the other root canal. FIG. 13B shows a latitudinal section of the tooth canal. At t=0s, the double helicoid-shaped soft robot is at a top of the tooth canal. The biohybrid robot then moves down the tooth canal until reaching the bottom of the tooth canal at t=17.7s. FIG. 13C depicts the eradication of biofilm in the isthmus by biohybrid robots as shown before and after treatment; the biofilms were fluorescently labelled for
visualization.
More generally, the disclosed techniques can be applied to eradicate bacteria within a biofilm matrix, degrade the matrix and remove biofilm debris on biotic surfaces such as teeth and mucosal surfaces, as well as abiotic surfaces such as implanted medical devices and catheters, or surgical instruments including endoscopes, cannulas/cannulae thereby preventing infections and medical complications in patients. Furthermore, the disclosed techniques can be applied to eradicate bacteria within a biofilm matrix, degrade the matrix and remove biofilm debris in natural and industrial settings such as man-made aquatic systems ( e.g ., cooling towers, pools, aquariums and spas), glass/plastic surfaces including windows and food packaging and the interiors of pipes, water lines and other enclosed surfaces.
The foregoing merely illustrates the principles of the disclosed subject matter. Various modifications and alterations to the described embodiments will be apparent to those skilled in the art in view of the teachings herein. It will thus be appreciated that those skilled in the art will be able to devise numerous techniques which, although not explicitly described herein, embody the principles of the disclosed subject matter and are thus within its spirit and scope.

Claims

1. A method for eradicating bacteria within a biofilm matrix, matrix degradation, and biofilm removal comprising:
administering a suspension of H2O2 and iron oxide nanoparticles to the biofilm having bacteria therein, wherein the suspension is adapted to substantially eradicate the bacteria and degrade the biofilm matrix;
actuating the iron oxide nanoparticles for assembly into biohybrid robots suitable for removal of biofilm debris caused by bacterial eradication and matrix degradation, and moving the biohybrid robots to remove the bio film debris from a surface.
2. The method of claim 1, wherein the suspension comprises between 500 micrograms and 5000 micrograms of iron oxide nanoparticles per milliliter of 50% glycerol.
3. The method of claim 2, wherein the suspension comprises at least one enzyme, adapted to degrade the bio film matrix.
4. The method of claim 3, wherein the at least one enzyme includes mutanase, dextranase, DNase, protease, lipase, amyloglucosidade, glucose oxidase, or combinations thereof.
5. The method of claim 2, wherein the suspension comprises 1% H2O2 and
1.75U/8.75U mutanase/dextranase.
6. The method of claim 1, wherein the actuating comprises applying a magnetic field to actuate the iron oxide nanoparticles to assemble into biohybrid robots.
7. The method of claim 6, wherein the moving comprises applying the magnetic field to move the biohybrid robots.
8. A system for eradicating bacteria within a biofilm matrix, matrix degradation, and biofilm removal comprising: a suspension of H2O2 and iron oxide nanoparticles, adapted to substantially eradicate the bacteria and degrade the biofilm matrix; and
a magnetic element, adapted to actuate the iron oxide nanoparticles for assembly into biohybrid robots suitable for removal of biofilm debris caused by bacterial eradication and matrix degradation.
9. The system of claim 8, wherein the suspension comprises 2000 micrograms of iron oxide nanoparticles per milliliter of 50% glycerol.
10. The system of claim 9, wherein the suspension comprises at least one enzyme, adapted to degrade the biofilm matrix.
11. The system of claim 10, wherein the at least one enzyme includes include mutanase and dextranase.
12. The system of claim 9, wherein the suspension comprises 1% H2O2 and
1.75U/8.75U mutanase/dextranase.
13. The system of claim 8, wherein the magnetic element comprises at least one of a permanent magnet or an array of electromagnets, adapted to apply a magnetic field to the biofilm to actuate the iron oxide nanoparticles to assemble into biohybrid robots.
14. The system of claim 13, wherein the permanent magnet moves the biohybrid robots, adapted to remove the biofilm debris from the biofilm matrix.
15. A method for eradicating bacteria within a biofilm matrix, matrix degradation, and biofilm removal, comprising:
embedding iron oxide nanoparticles in a hydrogel, adapted to form a soft robotic structure;
administering the soft robotic structure to a biofilm-covered surface; and magnetizing the soft robot structure, wherein the soft robotic structure is adapted to substantially eradicate the bacteria, degrade the biofilm matrix, and remove biofilm debris caused by biofilm eradication.
16. The method of claim 15, wherein the hydrogel is a stimuli-responsive polymer.
17. The method of claim 16, wherein the soft robotic structure is 3% weight by volume agar and 10% weight by volume iron oxide nanoparticles.
18. The method of claim 15, wherein the soft robotic structure, adapted to realign with a magnetic field direction, is magnetized along its short axis.
19. The method of claim 18, wherein the soft robotic structure is vane-shaped, adapted to scrape and displace the biofilm debris from a wall of an enclosed surface.
20. The method of claim 18, wherein the soft robotic structure is double helicoid shaped, adapted to drill through biofilm occlusions and clear biofilm from walls.
21. The method of claim 1 , wherein the suspension of H2O2 and iron oxide nanoparticles is administered to a tooth canal for endodontic disinfection or biofilm removal.
22. The method of claim 21, wherein the biohybrid robots are adapted to move through the isthmus to disrupt biofilms and remove the biofilm debris.
23. The system of claim 14, wherein the suspension of H2O2 and iron oxide nanoparticles is administered to a tooth canal for endodontic disinfection or biofilm removal.
24. The system of claim 21, wherein the biohybrid robots are adapted to move through the isthmus to disrupt biofilm and remove the biofilm debris.
25. The method of claim 20, further comprising moving the soft robotic structure across the tooth canal for endodontic disinfection or biofilm removal.
PCT/US2019/062941 2018-11-28 2019-11-25 Small-scale robots for biofilm eradication WO2020112601A1 (en)

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US17/291,326 US20220000119A1 (en) 2018-11-28 2019-11-25 Small-scale robots for biofilm eradication
CN201980078197.1A CN113194727A (en) 2018-11-28 2019-11-25 Small robot for eradicating biofilm
CA3119489A CA3119489A1 (en) 2018-11-28 2019-11-25 Small-scale robots for biofilm eradication
EP19890194.4A EP3886589A4 (en) 2018-11-28 2019-11-25 Small-scale robots for biofilm eradication
JP2021530103A JP2022510910A (en) 2018-11-28 2019-11-25 Small robots for eradicating biofilms
BR112021010037-7A BR112021010037A2 (en) 2018-11-28 2019-11-25 methods and system for eradicating bacteria within a biofilm matrix, matrix degradation and biofilm removal
KR1020217019435A KR20210098480A (en) 2018-11-28 2019-11-25 Small robot for biofilm removal
MX2021006072A MX2021006072A (en) 2018-11-28 2019-11-25 Small-scale robots for biofilm eradication.
IL283393A IL283393B1 (en) 2018-11-28 2019-11-25 Small-scale robots for biofilm eradication
AU2019388848A AU2019388848A1 (en) 2018-11-28 2019-11-25 Small-scale robots for biofilm eradication
ZA2021/04331A ZA202104331B (en) 2018-11-28 2021-06-23 Small-scale robots for biofilm eradication

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Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2021087088A1 (en) * 2019-10-29 2021-05-06 The Trustees Of The University Of Pennsylvania Automated and precise device for dental plaque detection, monitoring and removal
WO2022124581A1 (en) * 2020-12-11 2022-06-16 서강대학교산학협력단 Method for producing muscle bundle, and biohybrid robot using same

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IL283393A (en) 2021-07-29
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JP2022510910A (en) 2022-01-28
KR20210098480A (en) 2021-08-10
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BR112021010037A2 (en) 2021-08-17
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